1yjp_complete_refine_001.log

# Date 2018-06-11 Time 21:42:51 PDT -0700 (1528778571.04 s)
#phil __OFF__

Command line arguments: "1yjp_complete.pdb" "1yjp.mtz"

HOST = nwmoriarty-m63.local.dhcp.lbl.gov
HOSTTYPE = unknown
MACHTYPE = x86_64
OSTYPE = darwin
VENDOR = apple
USER = nigel
PID = 20074

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  Version: dev
  Release tag: svn+SVN
  User: nigel
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------

Phenix developers include:
  Paul Adams, Pavel Afonine, Gabor Bunkoczi, Tom Burnley, Vincent Chen, 
  Youval Dar, Ian Davis, Eli Draizen, Nathaniel Echols, Richard Gildea, 
  Piet Gros, Ralf Grosse-Kunstleve, Jeffrey Headd, Bradley Hintze, Li-Wei Hung, 
  Tom Ioerger, Dorothee Liebschner, Airlie McCoy, Erik McKee, Nigel Moriarty, 
  Robert Oeffner, Billy Poon, Randy Read, Jane Richardson, David Richardson, 
  Jim Sacchettini, Nicholas Sauter, Oleg Sobolev, Laurent Storoni, 
  Tom Terwilliger, Christopher Williams, Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxWidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS,
    MUSCLE, KSDSSP, PULCHRA, ANTLRv3
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

  No user-defined map coefficients or files defined; will use default map
  outputs instead.
Working crystal symmetry after inspecting all inputs:
  Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)
  Space group: P 1 21 1 (No. 4)


================================== X-ray data =================================

F-obs:
  1yjp.mtz:FOBS,SIGFOBS

Miller array info: 1yjp.mtz:FOBS,SIGFOBS
Observation type: xray.amplitude
Type of data: double, size=495
Type of sigmas: double, size=495
Number of Miller indices: 495
Anomalous flag: False
Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)
Space group: P 1 21 1 (No. 4)
Systematic absences: 0
Centric reflections: 199
Resolution range: 22.4416 1.80066
Completeness in resolution range: 0.895118
Completeness with d_max=infinity: 0.895118
Wavelength: 0.9750

Number of F-obs in resolution range:                   495
Number of F-obs<0 (these reflections will be rejected): 0
Number of F-obs=0 (these reflections will be used in refinement): 0
Refinement resolution range: d_max =  22.4416
                             d_min =   1.8007

R-free flags:
  1yjp.mtz:R-free-flags

Miller array info: 1yjp.mtz:R-free-flags
Observation type: None
Type of data: int, size=495
Type of sigmas: None
Number of Miller indices: 495
Anomalous flag: False
Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)
Space group: P 1 21 1 (No. 4)
Systematic absences: 0
Centric reflections: 199
Resolution range: 22.4416 1.80066
Completeness in resolution range: 0.895118
Completeness with d_max=infinity: 0.895118
Wavelength: 0.9750

Test (R-free flags) flag value: 0

Number of work/free reflections by resolution:
                                    work free  %free
  bin  1: 22.4433 -  3.8734 [61/70]   59    2   3.3%
  bin  2:  3.8734 -  3.0770 [53/58]   49    4   7.5%
  bin  3:  3.0770 -  2.6887 [49/55]   46    3   6.1%
  bin  4:  2.6887 -  2.4432 [37/40]   35    2   5.4%
  bin  5:  2.4432 -  2.2683 [62/66]   60    2   3.2%
  bin  6:  2.2683 -  2.1347 [51/56]   49    2   3.9%
  bin  7:  2.1347 -  2.0278 [50/55]   46    4   8.0%
  bin  8:  2.0278 -  1.9396 [49/56]   49    0   0.0%
  bin  9:  1.9396 -  1.8650 [43/50]   42    1   2.3%
  bin 10:  1.8650 -  1.8007 [40/47]   40    0   0.0%
                            overall  475   20   4.0%
  Monomer Library directory:
    "/Users/nigel/phenix/bootstrap/modules/chem_data/mon_lib"
  Total number of atoms: 128
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 107
          Classifications: {'peptide': 7}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 6}
    Chain: "A"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 21
          Classifications: {'water': 7}
          Link IDs: {None: 6}
  Time building chain proxies: 0.10, per 1000 atoms: 0.78
  Number of scatterers: 128
  At special positions: 0
  Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)
  Space group: P 1 21 1 (No. 4)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     O      21      8.00
     N      12      7.00
     C      33      6.00
     H      62      1.00
    sf(0) = scattering factor at diffraction angle 0.


No array of experimental phases found.


============================== Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   O      21      7.97       2
   N      12      6.97       2
   C      33      5.97       2
   H      62      1.00       2
  sf(0) = scattering factor at diffraction angle 0.


==================== Fixing bad ADP in input model (if any) ===================


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.
  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : False - 3.50
        Amimo acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.06
  Conformation dependent library (CDL) restraints added in 3.2 milliseconds
  
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  12

  Time building geometry restraints manager: 0.06 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     0.98: 62
        0.98 -     1.12: 0
        1.12 -     1.27: 13
        1.27 -     1.41: 18
        1.41 -     1.55: 28
  Bond restraints: 121
  Sorted by residual:
  bond pdb=" CA  GLN A   4 "
       pdb=" C   GLN A   4 "
    ideal  model  delta    sigma   weight residual
    1.522  1.553 -0.030 1.18e-02 7.18e+03 6.53e+00
  bond pdb=" N   GLN A   4 "
       pdb=" CA  GLN A   4 "
    ideal  model  delta    sigma   weight residual
    1.460  1.485 -0.025 1.17e-02 7.31e+03 4.40e+00
  bond pdb=" CA  ASN A   2 "
       pdb=" C   ASN A   2 "
    ideal  model  delta    sigma   weight residual
    1.524  1.498  0.025 1.26e-02 6.30e+03 4.00e+00
  bond pdb=" CA  ASN A   6 "
       pdb=" C   ASN A   6 "
    ideal  model  delta    sigma   weight residual
    1.526  1.504  0.022 1.28e-02 6.10e+03 2.85e+00
  bond pdb=" N   ASN A   2 "
       pdb=" CA  ASN A   2 "
    ideal  model  delta    sigma   weight residual
    1.456  1.475 -0.019 1.23e-02 6.61e+03 2.26e+00
  ... (remaining 116 not shown)

  Histogram of bond angle deviations from ideal:
      106.59 -   110.24: 81
      110.24 -   113.89: 25
      113.89 -   117.54: 15
      117.54 -   121.19: 46
      121.19 -   124.83: 24
  Bond angle restraints: 191
  Sorted by residual:
  angle pdb=" N   ASN A   3 "
        pdb=" CA  ASN A   3 "
        pdb=" C   ASN A   3 "
      ideal   model   delta    sigma   weight residual
     108.90  113.48   -4.58 1.63e+00 3.76e-01 7.90e+00
  angle pdb=" N   GLN A   4 "
        pdb=" CA  GLN A   4 "
        pdb=" C   GLN A   4 "
      ideal   model   delta    sigma   weight residual
     108.02  111.93   -3.91 1.78e+00 3.16e-01 4.84e+00
  angle pdb=" CA  GLN A   4 "
        pdb=" C   GLN A   4 "
        pdb=" O   GLN A   4 "
      ideal   model   delta    sigma   weight residual
     120.33  122.27   -1.94 1.08e+00 8.57e-01 3.23e+00
  angle pdb=" CA  GLN A   5 "
        pdb=" C   GLN A   5 "
        pdb=" O   GLN A   5 "
      ideal   model   delta    sigma   weight residual
     120.38  122.31   -1.93 1.09e+00 8.42e-01 3.13e+00
  angle pdb=" C   GLN A   4 "
        pdb=" N   GLN A   5 "
        pdb=" CA  GLN A   5 "
      ideal   model   delta    sigma   weight residual
     123.00  120.57    2.43 1.38e+00 5.25e-01 3.09e+00
  ... (remaining 186 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.03 -    14.50: 36
       14.50 -    28.97: 5
       28.97 -    43.45: 1
       43.45 -    57.92: 1
       57.92 -    72.39: 1
  Dihedral angle restraints: 44
    sinusoidal: 21
      harmonic: 23
  Sorted by residual:
  dihedral pdb=" CA  ASN A   3 "
           pdb=" C   ASN A   3 "
           pdb=" N   GLN A   4 "
           pdb=" CA  GLN A   4 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  166.21   13.79     0      5.00e+00 4.00e-02 7.60e+00
  dihedral pdb=" CB  GLN A   5 "
           pdb=" CG  GLN A   5 "
           pdb=" CD  GLN A   5 "
           pdb=" OE1 GLN A   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -72.39   72.39     2      3.00e+01 1.11e-03 4.85e+00
  dihedral pdb=" CB  GLN A   4 "
           pdb=" CG  GLN A   4 "
           pdb=" CD  GLN A   4 "
           pdb=" OE1 GLN A   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   54.08  -54.08     2      3.00e+01 1.11e-03 3.50e+00
  ... (remaining 41 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 1
       0.024 -    0.047: 1
       0.047 -    0.071: 1
       0.071 -    0.094: 1
       0.094 -    0.118: 2
  Chirality restraints: 6
  Sorted by residual:
  chirality pdb=" CA  GLN A   5 "
            pdb=" N   GLN A   5 "
            pdb=" C   GLN A   5 "
            pdb=" CB  GLN A   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.48e-01
  chirality pdb=" CA  ASN A   6 "
            pdb=" N   ASN A   6 "
            pdb=" C   ASN A   6 "
            pdb=" CB  ASN A   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.62   -0.11 2.00e-01 2.50e+01 2.86e-01
  chirality pdb=" CA  ASN A   2 "
            pdb=" N   ASN A   2 "
            pdb=" C   ASN A   2 "
            pdb=" CB  ASN A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.43    0.08 2.00e-01 2.50e+01 1.80e-01
  ... (remaining 3 not shown)

  Planarity restraints: 19
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A   7 "   -0.007 2.00e-02 2.50e+03   7.94e-03 1.89e+00
        pdb=" CG  TYR A   7 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR A   7 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR A   7 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR A   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A   7 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR A   7 "   -0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR A   7 "    0.007 2.00e-02 2.50e+03
        pdb=" HD1 TYR A   7 "    0.001 2.00e-02 2.50e+03
        pdb=" HD2 TYR A   7 "    0.001 2.00e-02 2.50e+03
        pdb=" HE1 TYR A   7 "   -0.002 2.00e-02 2.50e+03
        pdb=" HE2 TYR A   7 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A   2 "    0.006 2.00e-02 2.50e+03   9.73e-03 1.42e+00
        pdb=" CG  ASN A   2 "   -0.021 2.00e-02 2.50e+03
        pdb=" OD1 ASN A   2 "    0.008 2.00e-02 2.50e+03
        pdb=" ND2 ASN A   2 "    0.007 2.00e-02 2.50e+03
        pdb="HD21 ASN A   2 "    0.000 2.00e-02 2.50e+03
        pdb="HD22 ASN A   2 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A   4 "    0.005 2.00e-02 2.50e+03   1.09e-02 1.18e+00
        pdb=" C   GLN A   4 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   GLN A   4 "    0.007 2.00e-02 2.50e+03
        pdb=" N   GLN A   5 "    0.006 2.00e-02 2.50e+03
  ... (remaining 16 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.28: 61
        2.28 -     2.83: 291
        2.83 -     3.39: 554
        3.39 -     3.94: 934
        3.94 -     4.50: 1207
  Nonbonded interactions: 3047
  Sorted by model distance:
  nonbonded pdb=" HH  TYR A   7 "
            pdb=" O   HOH A  11 "
     model   vdw sym.op.
     1.719 1.850 -x+1,y-1/2,-z+1
  nonbonded pdb=" O   HOH A  11 "
            pdb=" HH  TYR A   7 "
     model   vdw sym.op.
     1.719 1.850 -x+1,y+1/2,-z+1
  nonbonded pdb=" OD1 ASN A   3 "
            pdb="HD22 ASN A   3 "
     model   vdw sym.op.
     1.859 1.850 x,y+1,z
  nonbonded pdb=" H2  GLY A   1 "
            pdb=" OXT TYR A   7 "
     model   vdw sym.op.
     1.869 1.850 x-1,y,z
  nonbonded pdb="HD21 ASN A   3 "
            pdb=" OE1 GLN A   5 "
     model   vdw
     1.876 1.850
  ... (remaining 3042 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

======================== Summary of geometry restraints =======================


====================== Modifying start model if requested =====================

n_use            =  128
n_use_u_iso      =  128
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
total number of scatterers =  128

================== Extract refinement strategy and selections =================

Refinement flags and selection counts:
  individual_sites       =  True (128 atoms)
  torsion_angles         = False (0 atoms)
  rigid_body             = False (0 atoms in 0 groups)
  individual_adp         =  True (iso = 128 aniso = 0)
  group_adp              = False (0 atoms in 0 groups)
  tls                    = False (0 atoms in 0 groups)
  occupancies            =  True (0 atoms)
  group_anomalous        = False

*******************************************************************************
Automatic adjustment:
  hydrogens.refine=riding
*******************************************************************************


==================== Process input NCS or/and find new NCS ====================

Using existing and finding new NCS is disabled.
Use ncs_search.enabled=true to activate it.
Look at refinement.ncs for more NCS related parameters.

=================== Write initial parameters into .eff file ===================

Writing effective parameters to file:
  /Users/nigel/qr/qr-tests-1yjp/1yjp_complete_refine_001.eff

Writing geometry restraints to file:
  /Users/nigel/qr/qr-tests-1yjp/1yjp_complete_refine_001.geo
CPU time processing inputs: 5.09


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 21.93700027 4.866000175 23.47699928 90 107.0800018 90
    space_group = "P 1 21 1"
  }
  input {
    pdb {
      file_name = "1yjp_complete.pdb"
    }
    xray_data {
      file_name = "1yjp.mtz"
      labels = "FOBS,SIGFOBS"
      r_free_flags {
        file_name = "1yjp.mtz"
        label = "R-free-flags"
        test_flag_value = 0
      }
    }
  }
  output {
    prefix = "1yjp_complete_refine"
    serial = 1
  }
  electron_density_maps {
    map_coefficients {
      map_type = "2mFo-DFc"
      mtz_label_amplitudes = "2FOFCWT"
      mtz_label_phases = "PH2FOFCWT"
      fill_missing_f_obs = True
    }
    map_coefficients {
      map_type = "2mFo-DFc"
      mtz_label_amplitudes = "2FOFCWT_no_fill"
      mtz_label_phases = "PH2FOFCWT_no_fill"
    }
    map_coefficients {
      map_type = "mFo-DFc"
      mtz_label_amplitudes = "FOFCWT"
      mtz_label_phases = "PHFOFCWT"
    }
    map_coefficients {
      map_type = "anomalous"
      mtz_label_amplitudes = "ANOM"
      mtz_label_phases = "PANOM"
    }
    map {
      map_type = "2mFo-DFc"
      fill_missing_f_obs = True
    }
    map {
      map_type = "2mFo-DFc"
    }
    map {
      map_type = "mFo-DFc"
    }
  }
  hydrogens {
    refine = individual *riding Auto
  }
}
#phil __OFF__


=============================== refinement start ==============================


================================== Hydrogens ==================================

Total:
  count: 62
  occupancy sum:  62.00 (% of total atoms  48.44)
Rotatable:
  count: 4
  occupancy sum:   4.00 (% of total atoms   3.12)

   ----------structure factors based statistics (before refinement)----------  


                         ----------X-ray data----------                        

|--(resolution: 1.80 - 22.44 A, n_refl.=495 (all), 4.04  % free)--------------|
|                                                                             |
| r_work= 0.2172 r_free= 0.2297 coordinate error (max.-lik. estimate): 0.00 A |
|                                                                             |
| normalized target function (ls_wunit_k1) (work): 0.055142                   |
| target function (ls_wunit_k1) not normalized (work): 26.192317              |
| target function (ls_wunit_k1) not normalized (free): 1.083295               |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 22.4433 -  1.8007 0.90    475   20 0.2172 0.2297      26.223      47.311|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 22.4433 -  1.8007   475    20  0.87  16.75   1.00     0.66         40.35|
|alpha:            min =        0.62 max =            0.70 mean =         0.66|
|beta:             min =       22.20 max =           63.63 mean =        40.35|
|figures of merit: min =        0.05 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           85.20 mean =        16.75|
|phase err.(test): min =        0.00 max =           44.93 mean =        10.68|
|-----------------------------------------------------------------------------|

        ----------Initial model statistics (before refinement)----------       


                min    max   mean <Bi,j>   iso aniso
   Overall:    8.86  43.49  14.67   1.31    66     0
   Protein:    8.86  17.49  13.15   1.31    59     0
   Water:     17.08  43.49  27.46    N/A     7     0
   Chain  A:   8.86  43.49  14.67    N/A    66     0
   Histogram:
       Values      Number of atoms
     8.86 - 12.32        26
    12.32 - 15.79        26
    15.79 - 19.25         8
    19.25 - 22.71         2
    22.71 - 26.18         2
    26.18 - 29.64         0
    29.64 - 33.10         0
    33.10 - 36.56         0
    36.56 - 40.03         1
    40.03 - 43.49         1

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 1.00   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 3 *************************

|--(resolution: 1.80 - 22.44 A, n_refl.=495 (all), 4.04  % free)--------------|
|                                                                             |
| r_work= 0.2172 r_free= 0.2297 coordinate error (max.-lik. estimate): 0.00 A |
|                                                                             |
| normalized target function (ls_wunit_k1) (work): 0.055142                   |
| target function (ls_wunit_k1) not normalized (work): 26.192317              |
| target function (ls_wunit_k1) not normalized (free): 1.083295               |
|-----------------------------------------------------------------------------|

=========================== Bulk-solvent and scaling ==========================


============================= updating all scales =============================

                   start: r(all,work,free)=0.2178 0.2172 0.2297 n_refl.: 495
       re-set all scales: r(all,work,free)=0.2178 0.2172 0.2297 n_refl.: 495
         remove outliers: r(all,work,free)=0.2219 0.2215 0.2297 n_refl.: 493
 overall B=0.00 to atoms: r(all,work,free)=0.2219 0.2215 0.2297 n_refl.: 493
bulk-solvent and scaling: r(all,work,free)=0.1754 0.1745 0.1904 n_refl.: 493
         remove outliers: r(all,work,free)=0.1754 0.1745 0.1904 n_refl.: 493

======================== Statistics in resolution bins ======================== 

Total model structure factor:
  F_model = k_total * (F_calc + k_mask * F_mask)

    k_total = k_isotropic * k_anisotropic
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 22.442-3.252    87.83    95     6 0.1566    29.059    28.146 1.010 1.042 0.254
  3.247-2.435    90.00    94     5 0.1700    20.193    19.864 0.970 0.987 0.107
  2.435-1.801    89.60   284     9 0.1919    11.843    11.294 1.026 0.993 0.060

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=1.0577   b_overall=1.2827  

============================ Set refinement target ============================

  using refinement target ls_wunit_k1 


================================== NQH flips ==================================

r_work=0.1745 r_free=0.1904
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
r_work=0.1745 r_free=0.1904

==================== Compute data/restraints target weights ===================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.951060              wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.240714              wxu_scale = 1.000            wu = 1.000         |
|-----------------------------------------------------------------------------|


====================== XYZ individual (reciprocal space) ======================

    R-FACTORS           RMSD     CLASH  RAMA  ROTA CBET WEIGHT    TARGETS
 work  free  delta  bonds  angl                                  data   restr
17.45 19.04   1.58  0.014   1.4    0.0   0.0   0.0    0   none  0.037  0.0464
17.45 17.02  -0.43  0.009   1.0    0.0   0.0   0.0    0  3.976  0.033  0.0234

Legend:
  - first line corresponds to starting state (before refinement)
  - R-factors reported in percent
  - delta is Rfree-Rwork in percent
  - CLASH is all-atom Molprobity clashscore
  - ROTA is percent of side-chain rotamer outliers
  - RAMA is percent of Ramachandran plot outliers
  - CBET is number of Cbeta deviations
  - WEIGHT is relative weight between X-ray (or neutron) target and restraints
  - TARGETS: the values of X-ray (or neutron) and restraints target functions

====================== ADP refinement (reciprocal space) ======================


                 ----------Individual ADP refinement----------                 

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
17.45 17.02  -0.43  0.913  15.369  0.241    0.033
16.67 16.12  -0.55  1.812  15.447  0.241    0.030

                min    max   mean <Bi,j>   iso aniso
   Overall:    8.05  43.95  14.82   2.07    66     0
   Protein:    8.05  20.73  13.23   2.07    59     0
   Water:     18.29  43.95  28.21    N/A     7     0
   Chain  A:   8.05  43.95  14.82    N/A    66     0
   Histogram:
       Values      Number of atoms
     8.05 - 11.64        17
    11.64 - 15.23        30
    15.23 - 18.82        11
    18.82 - 22.41         2
    22.41 - 26.00         3
    26.00 - 29.59         1
    29.59 - 33.18         0
    33.18 - 36.77         0
    36.77 - 40.36         1
    40.36 - 43.95         1


=========================== Idealize ADP of riding H ==========================

r_work=0.1667 r_free=0.1612
r_work=0.1668 r_free=0.1606

*********************** REFINEMENT MACRO_CYCLE 2 OF 3 *************************

|--(resolution: 1.80 - 22.44 A, n_refl.=493 (all), 4.06  % free)--------------|
|                                                                             |
| r_work= 0.1668 r_free= 0.1606 coordinate error (max.-lik. estimate): 0.10 A |
|                                                                             |
| normalized target function (ls_wunit_k1) (work): 0.030370                   |
| target function (ls_wunit_k1) not normalized (work): 14.365223              |
| target function (ls_wunit_k1) not normalized (free): 0.525019               |
|-----------------------------------------------------------------------------|

=========================== Bulk-solvent and scaling ==========================


============================= updating all scales =============================

                   start: r(all,work,free)=0.1665 0.1668 0.1606 n_refl.: 493
       re-set all scales: r(all,work,free)=0.2133 0.2138 0.1980 n_refl.: 493
         remove outliers: r(all,work,free)=0.2133 0.2138 0.1980 n_refl.: 493
 overall B=0.00 to atoms: r(all,work,free)=0.2133 0.2138 0.1980 n_refl.: 493
bulk-solvent and scaling: r(all,work,free)=0.1652 0.1659 0.1532 n_refl.: 493
         remove outliers: r(all,work,free)=0.1652 0.1659 0.1532 n_refl.: 493

======================== Statistics in resolution bins ======================== 

Total model structure factor:
  F_model = k_total * (F_calc + k_mask * F_mask)

    k_total = k_isotropic * k_anisotropic
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 22.442-3.252    87.83    95     6 0.1326    29.059    28.524 1.084 0.939 0.380
  3.247-2.435    90.00    94     5 0.1435    20.193    20.112 1.049 0.910 0.110
  2.435-1.801    89.60   284     9 0.2056    11.843    11.438 1.067 0.950 0.070

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=1.0185   b_overall=0.6655  

============================ Set refinement target ============================

  using refinement target ls_wunit_k1 


============================ Update CDL restraints ============================


================================== NQH flips ==================================

r_work=0.1659 r_free=0.1532
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
r_work=0.1659 r_free=0.1532

==================== Compute data/restraints target weights ===================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.744021              wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.217475              wxu_scale = 1.000            wu = 1.000         |
|-----------------------------------------------------------------------------|


====================== XYZ individual (reciprocal space) ======================

    R-FACTORS           RMSD     CLASH  RAMA  ROTA CBET WEIGHT    TARGETS
 work  free  delta  bonds  angl                                  data   restr
16.59 15.32  -1.26  0.009   1.0    0.0   0.0   0.0    0   none  0.030  0.0235
16.63 13.67  -2.95  0.008   1.0    0.0   0.0   0.0    0  4.372  0.030  0.0223

Legend:
  - first line corresponds to starting state (before refinement)
  - R-factors reported in percent
  - delta is Rfree-Rwork in percent
  - CLASH is all-atom Molprobity clashscore
  - ROTA is percent of side-chain rotamer outliers
  - RAMA is percent of Ramachandran plot outliers
  - CBET is number of Cbeta deviations
  - WEIGHT is relative weight between X-ray (or neutron) target and restraints
  - TARGETS: the values of X-ray (or neutron) and restraints target functions

====================== ADP refinement (reciprocal space) ======================


                 ----------Individual ADP refinement----------                 

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
16.63 13.67  -2.95  3.015  17.357  0.217    0.030
16.68 13.63  -3.04  3.088  17.723  0.217    0.030

                min    max   mean <Bi,j>   iso aniso
   Overall:    8.87  39.91  15.52   1.95    66     0
   Protein:    8.87  23.16  14.11   1.95    59     0
   Water:     17.98  39.91  27.47    N/A     7     0
   Chain  A:   8.87  39.91  15.52    N/A    66     0
   Histogram:
       Values      Number of atoms
     8.87 - 11.97        18
    11.97 - 15.08        19
    15.08 - 18.18        17
    18.18 - 21.29         5
    21.29 - 24.39         3
    24.39 - 27.50         1
    27.50 - 30.60         1
    30.60 - 33.71         0
    33.71 - 36.81         1
    36.81 - 39.91         1


=========================== Idealize ADP of riding H ==========================

r_work=0.1668 r_free=0.1363
r_work=0.1668 r_free=0.1354

*********************** REFINEMENT MACRO_CYCLE 3 OF 3 *************************

|--(resolution: 1.80 - 22.44 A, n_refl.=493 (all), 4.06  % free)--------------|
|                                                                             |
| r_work= 0.1668 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.00 A |
|                                                                             |
| normalized target function (ls_wunit_k1) (work): 0.029475                   |
| target function (ls_wunit_k1) not normalized (work): 13.941894              |
| target function (ls_wunit_k1) not normalized (free): 0.381005               |
|-----------------------------------------------------------------------------|

=========================== Bulk-solvent and scaling ==========================


============================= updating all scales =============================

                   start: r(all,work,free)=0.1653 0.1668 0.1354 n_refl.: 493
       re-set all scales: r(all,work,free)=0.2149 0.2156 0.1859 n_refl.: 493
         remove outliers: r(all,work,free)=0.2149 0.2156 0.1859 n_refl.: 493
overall B=-0.11 to atoms: r(all,work,free)=0.2147 0.2155 0.1854 n_refl.: 493
bulk-solvent and scaling: r(all,work,free)=0.1649 0.1663 0.1359 n_refl.: 493
         remove outliers: r(all,work,free)=0.1649 0.1663 0.1359 n_refl.: 493

======================== Statistics in resolution bins ======================== 

Total model structure factor:
  F_model = k_total * (F_calc + k_mask * F_mask)

    k_total = k_isotropic * k_anisotropic
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 22.442-3.252    87.83    95     6 0.1275    29.059    28.631 1.003 1.030 0.434
  3.247-2.435    90.00    94     5 0.1489    20.193    20.049 0.988 0.990 0.000
  2.435-1.801    89.60   284     9 0.2077    11.843    11.430 1.037 1.022 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=1.0231   b_overall=0.0125  

============================ Set refinement target ============================

  using refinement target ls_wunit_k1 


============================ Update CDL restraints ============================


============================= Setup riding H model ============================

  Before: r_work=0.1663 r_free=0.1359
  After: r_work=0.1666 r_free=0.1363

================================== NQH flips ==================================

r_work=0.1666 r_free=0.1363
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
r_work=0.1666 r_free=0.1363

==================== Compute data/restraints target weights ===================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.086115             wxc_scale = 0.500            wc = 1.000         |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.196386              wxu_scale = 1.000            wu = 1.000         |
|-----------------------------------------------------------------------------|


====================== XYZ individual (reciprocal space) ======================

    R-FACTORS           RMSD     CLASH  RAMA  ROTA CBET WEIGHT    TARGETS
 work  free  delta  bonds  angl                                  data   restr
16.66 13.63  -3.03  0.008   1.0    0.0   0.0   0.0    0   none  0.030  0.0236
16.65 13.65  -3.01  0.008   1.0    0.0   0.0   0.0    0  5.043  0.030  0.0236

Legend:
  - first line corresponds to starting state (before refinement)
  - R-factors reported in percent
  - delta is Rfree-Rwork in percent
  - CLASH is all-atom Molprobity clashscore
  - ROTA is percent of side-chain rotamer outliers
  - RAMA is percent of Ramachandran plot outliers
  - CBET is number of Cbeta deviations
  - WEIGHT is relative weight between X-ray (or neutron) target and restraints
  - TARGETS: the values of X-ray (or neutron) and restraints target functions

====================== ADP refinement (reciprocal space) ======================


                 ----------Individual ADP refinement----------                 

    R-FACTORS      <Bi-Bj>  <B>   WEIGHT       TARGETS
 work  free  delta                           data restr
16.65 13.65  -3.01  2.997  17.944  0.196    0.030
16.72 13.77  -2.94  2.687  18.369  0.196    0.030

                min    max   mean <Bi,j>   iso aniso
   Overall:    9.48  38.67  16.24   1.92    66     0
   Protein:    9.48  23.38  14.88   1.92    59     0
   Water:     18.82  38.67  27.65    N/A     7     0
   Chain  A:   9.48  38.67  16.24    N/A    66     0
   Histogram:
       Values      Number of atoms
     9.48 - 12.40        13
    12.40 - 15.32        22
    15.32 - 18.24        17
    18.24 - 21.16         6
    21.16 - 24.08         3
    24.08 - 26.99         2
    26.99 - 29.91         1
    29.91 - 32.83         0
    32.83 - 35.75         1
    35.75 - 38.67         1


=========================== Idealize ADP of riding H ==========================

r_work=0.1672 r_free=0.1377
r_work=0.1675 r_free=0.1376

                         ----------X-ray data----------                        

|--(resolution: 1.80 - 22.44 A, n_refl.=493 (all), 4.06  % free)--------------|
|                                                                             |
| r_work= 0.1675 r_free= 0.1376 coordinate error (max.-lik. estimate): 0.00 A |
|                                                                             |
| normalized target function (ls_wunit_k1) (work): 0.029677                   |
| target function (ls_wunit_k1) not normalized (work): 14.037125              |
| target function (ls_wunit_k1) not normalized (free): 0.385860               |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 22.4433 -  1.8007 0.89    473   20 0.1675 0.1376      13.148      16.852|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 22.4433 -  1.8007   473    20  0.92  11.90   1.00     0.71         21.98|
|alpha:            min =        0.67 max =            0.73 mean =         0.71|
|beta:             min =       17.75 max =           27.73 mean =        21.98|
|figures of merit: min =        0.09 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           81.82 mean =        11.90|
|phase err.(test): min =        0.00 max =           46.95 mean =         8.37|
|-----------------------------------------------------------------------------|

==================================== Final ====================================


============================= updating all scales =============================

                   start: r(all,work,free)=0.1661 0.1675 0.1376 n_refl.: 493
       re-set all scales: r(all,work,free)=0.2178 0.2185 0.1923 n_refl.: 493
         remove outliers: r(all,work,free)=0.2178 0.2185 0.1923 n_refl.: 493
overall B=-1.20 to atoms: r(all,work,free)=0.2156 0.2165 0.1870 n_refl.: 493
bulk-solvent and scaling: r(all,work,free)=0.1656 0.1670 0.1358 n_refl.: 493
         remove outliers: r(all,work,free)=0.1656 0.1670 0.1358 n_refl.: 493

======================== Statistics in resolution bins ======================== 

Total model structure factor:
  F_model = k_total * (F_calc + k_mask * F_mask)

    k_total = k_isotropic * k_anisotropic
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 22.442-3.252    87.83    95     6 0.1280    29.059    28.636 1.074 0.959 0.446
  3.247-2.435    90.00    94     5 0.1512    20.193    20.051 1.048 0.922 0.000
  2.435-1.801    89.60   284     9 0.2079    11.843    11.417 1.090 0.952 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=1.0265   b_overall=0.4394  

================= overall refinement statistics: step by step =================

****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle                     
0    : statistics at the very beginning when nothing is done yet        
1_bss: bulk solvent correction and/or (anisotropic) scaling             
1_xyz: refinement of coordinates                                        
1_adp: refinement of ADPs (Atomic Displacement Parameters)              
1_occ: refinement of occupancies                                        
------------------------------------------------------------------------
 stage       r-work r-free bonds angles b_min b_max b_ave n_water shift
      0    : 0.2172 0.2297 0.014  1.35   8.9  43.5  14.7  21      0.000
      1_bss: 0.1745 0.1904 0.014  1.35   8.9  43.5  14.7  21      0.000
1_settarget: 0.1745 0.1904 0.014  1.35   8.9  43.5  14.7  21      0.000
      1_nqh: 0.1745 0.1904 0.014  1.35   8.9  43.5  14.7  21      0.000
   1_weight: 0.1745 0.1904 0.014  1.35   8.9  43.5  14.7  21      0.000
   1_xyzrec: 0.1745 0.1702 0.009  1.01   8.9  43.5  14.7  21      0.070
      1_adp: 0.1667 0.1612 0.009  1.01   8.1  44.0  14.8  21      0.070
  1_regHadp: 0.1668 0.1606 0.009  1.01   8.1  44.0  14.8  21      0.070
      2_bss: 0.1659 0.1532 0.009  1.01   8.1  44.0  14.8  21      0.070
2_settarget: 0.1659 0.1532 0.009  1.01   8.1  44.0  14.8  21      0.070
2_updatecdl: 0.1659 0.1532 0.009  1.01   8.1  44.0  14.8  21      0.070
      2_nqh: 0.1659 0.1532 0.009  1.01   8.1  44.0  14.8  21      0.070
   2_weight: 0.1659 0.1532 0.009  1.01   8.1  44.0  14.8  21      0.070
   2_xyzrec: 0.1663 0.1367 0.008  1.03   8.1  44.0  14.8  21      0.099
      2_adp: 0.1668 0.1363 0.008  1.03   8.9  39.9  15.5  21      0.099
  2_regHadp: 0.1668 0.1354 0.008  1.03   8.9  39.9  15.5  21      0.099
      3_bss: 0.1663 0.1359 0.008  1.03   8.8  39.8  15.4  21      0.099
3_settarget: 0.1663 0.1359 0.008  1.03   8.8  39.8  15.4  21      0.099
3_updatecdl: 0.1663 0.1359 0.008  1.03   8.8  39.8  15.4  21      0.099
    3_setrh: 0.1666 0.1363 0.008  1.03   8.8  39.8  15.4  21      0.100
      3_nqh: 0.1666 0.1363 0.008  1.03   8.8  39.8  15.4  21      0.100
   3_weight: 0.1666 0.1363 0.008  1.03   8.8  39.8  15.4  21      0.100
   3_xyzrec: 0.1665 0.1365 0.008  1.04   8.8  39.8  15.4  21      0.100
      3_adp: 0.1672 0.1377 0.008  1.04   9.5  38.7  16.2  21      0.100
  3_regHadp: 0.1675 0.1376 0.008  1.04   9.5  38.7  16.2  21      0.100
        end: 0.1670 0.1358 0.008  1.04   8.3  37.5  15.0  21      0.100
------------------------------------------------------------------------

CPU time actual refinement: 11.24


============================== Exporting results ==============================

Writing refined structure to PDB file:
  /Users/nigel/qr/qr-tests-1yjp/1yjp_complete_refine_001.pdb
n_use            =  128
n_use_u_iso      =  128
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
total number of scatterers =  128

Writing default parameters for subsequent refinement:
  /Users/nigel/qr/qr-tests-1yjp/1yjp_complete_refine_002.def


=============================== Detailed timings ==============================

  Micro-tasks:
    mask                            = 0.00   
    f_calc                          = 0.00   
    alpha_beta                      = 0.00   
    target                          = 0.00   
    gradients_wrt_atomic_parameters = 0.00   
    fmodel                         = 0.00   
    r_factors                      = 0.01   
    phase_errors                   = 0.02   
    foms                           = 0.00   
    TOTAL for micro-tasks          = 0.03   
NUMBER OF MASK CALCS=  0
Total CPU time: 18.01 seconds
from_scatterers_fft:    227 calls, 0.31 s
gradients_fft:          171 calls, 0.22 s

=========================== phenix.refine: finished ===========================

# Date 2018-06-11 Time 21:43:09 PDT -0700 (1528778589.85 s)
wall clock time: 20.28 s

Start R-work = 0.1745, R-free = 0.1904
Final R-work = 0.1670, R-free = 0.1358